Table Of Content

Table of Contents n Page Summary ..................................................................................... 2 Introduction . . . . . . . . . .. . . . . . . . . . . . . . . . . . .. .. . . .. . . . .. . . . . . .. .. . . .. .. . . . . .. . . . . . .. . . . .. . . .. . . .. 3 Members and personnel .. . . . . . . . .. . .. . .. .. . .. . . . . . . . . .. . . . .. . . . . . . . . .. .. .. .. .. .. . . . . . . .. 4 Management structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Construction of BioChem Pharma Genomics Facility . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Research support . . . . . . .. .. . . . . . . . . . . . . . . .. . .. . . . .. . .. .. .. . . . . . .. . .. .. . . . . .. . . .. .. . . . . . . . .. 7 Equipment acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Operation and maintenance ............................................................ 10 Bioinformatics infrastructure ............................................................ 11 Research programs ....................................................................... 12 Research training .......................................................................... 13 Seminars and workshops ................................. ............................... 16 Collaborations and linkages ............................................................. 20 Contributions and impact ................................................................ 22 Direct and indirect support .............................................................. 26 Future plans ................................................................................. 27 Appendices Appendix I - Plans for new genomics facility Appendix II - Plans for new programs 1 Summary The 1999-2000 academic year was the first full year of operation for the Centre for Structural and Functional Genomics. In the past year the Centre has made enormous progress towards the establishment of a research facility and in providing research training. We received an institutional innovation grant of over three million dollars from the Canada Foundation for Innovation. Members of the Centre have also received several genomics grants and contracts. Approximately 1,600 square feet of space on the twelfth floor of the Hall Building has been converted into a biotechnology laboratory, a bioinformatics laboratory, a computational server room and an image facility. This suite of rooms forms the core of the BioChem Pharma Genomics Facility. Over $1.2M have been used to acquire large and small equipment. Major instruments that have been acquired include an automated DNA sequencer, an analytical ultracentrifuge, a laser scanning confocal microscope, isothermal titration microcalorimeter, and a microarrayer for DNA chip technology. The Centre has held over 20 seminars and workshops to promote genomics research, and to provide theoretical background and hands-on research training in the use of various instruments. Discussions are underway to turn the workshops into intensive, credited courses to be offered in May and September of P.nc:h yP-;:ir A task force was set up to assess teaching programs in genomics and proteomics at the undergraduate and graduate levels. These are expected to be co op progr3ms where the students will receive part of their research training in industrial and government laboratorif?~. Future plans include increasing the membership of the Centre, expanding the proteomic3 platform, and 3col<ing additional funding for operation. 2 1 Introduction In November 1998, the faculty council of Arts and Science approved the formation of the Centre for Structural and Functional Genomics. The aims of the Centre are to: 1) create an intellectual environment for interdisciplinary research n on genomics; 2) establish infrastructures for biotechnology and bioinformatics; 3) foster collaborations and links with the industrial sector; and 4) support teaching programs and research training in genomics. Genomics encompasses an extremely broad domain. The Centre promotes basic and applied research programs on model organisms and microorganisms of economic relevance. The research programs focus on five aspects of functional genomics: 1) gene discovery, 2) gene function and expression, 3) localization of gene products, 4) molecular interactions, and 5) bioinformatics. These areas are envisioned to provide a multi-faceted strategy needed to understand how organisms function at the molecular level. They also form the conceptual framework in the design of new products, in the improvement of industrial practices, and in devising new strategies to remove environmental wastes. Through the Capital Campaign, Concordia received a donation of $1 M from BioChem Pharma Inc. and $100,000 from Dr. Francesco Bellini to establish a genomics facility. Managing the BioChem Pharma Genomics Facility is one of the main responsibilities of the Centre. 3 J Members and Personnel Initial membership was solicited from members of the Faculty of Arts and Science who were interested in genomics research, committed to work in an interdisciplinary environment, and were members of existing research teams. Several researchers who did not fulfill all the above criteria were invited to join as associate members. Full members: Dr. Patrick Gulick, Department of Biology Dr. Ragai Ibrahim, Department of Biology Dr. Paul Joyce, Department of Chemistry and Biochemistry Dr. Justin Pawlowski, Department of Chemistry and Biochemistry Dr. Reginald Storms, Department of Biology Dr. Adrian Tsang, Department of Biology Dr. Joanne Turnbull, Department of Chemistry and Biochemistry Dr. Luc Varin, Department of Biology Associate members: Dr. Carolyn Beckman, Department of Biology Dr. Howard Bussey, Department of Biology (McGill University) ] Dr. Gregory Butler, Faculty of Engineering and Computer Science Dr. Jack Kornblatt, Department of Biology Dr. Clement Lam, Faculty of Engineering and Computer Science The Centre provides support in biotechnology and bioinformatics. Our support staff is a mix of experienced technologists and trainees. Ms. Rawlings has been invaluable in maintaining records and facilitating the acquisition of equipment. In the past year, we encountered a high turnover of personnel primarily because our trained personnel were offered more lucrative positions elsewhere. Biotechnology: Nathalie Brodeur, B.Sc., January 2000 - Marielle Carpenter, B.Sc., January 1999- May 2000 Sonia Ruiz, M.Sc., January 1999 - February 2000 Alex Spurmanis, M.Sc., January 2000 - Peter Ulycznyi, Ph.D., April 2000 - Bioinformatics: Ainsley Archer, M.Sc., January 2000 -April 2000 Shawn Delaney, M.Sc., January 1999 - May 1999 Peter Wilkinson, B.Sc., May 1999 - Secretary· Kathryn Rawlings, March 1 t)t)t) - 4 Management Structure The management team is made up of a director and a scientific committee. Since inception, the director has been Dr. A. Tsang with Ors. G. Butler, P. Joyce and R. Storms as members of the scientific committee. The management team is in charge of all scientific aspects of the Centre including the management of the BioChem Pharma Genomics facility, initiating interdisciplinary research programs, promoting interactions between the Centre and other research institutions and industries, and designing interdisciplinary courses at the graduate and senior undergraduate levels. The director is responsible for the day-to-day operation of the Centre. The director reports to the Dean of Arts and Science. In September 1999, Dr. M. Singer, the Dean of Arts and Science, set up a task force to assess the needs of genomics research and teaching at Concordia. The task force also serves as a liaison between the Centre and other academic units in the University. The diagrams below illustrate the relationships among the various entities. I Dean of Arts and Science I / ~ Genomics Advisory Task Force: Centre for Structural & Functional • Vice-Dean Academic Genomics Scientific Committee: • Chair of Biology • Greg Butler ► • Chair of Chemistry/Biochemistry • Paul Joyce • Chair of Computer Science • Reg Storms • Director of Genomics Centre • Adrian Tsang ! 810Chem Pharma Genomics Centre: • Biotechnology lab • Bioinformatics lab • Computational network 5 BioChem Pharma Genomics Facility In November 1999, Mr. Charles Emond, the Vice-Rector Services, approved the ih conversion of two classrooms on the 1 floor of the Hall Building into laboratories for the BioChem Pharma Genomics Facility. In January 2000, Mr. Emond finalized arrangements with the Registrar to accommodate courses that occupied these rooms. The two adjoining classrooms (H 1221 and H 1223) have a total space of 1,600 square feet. Dr. Martin Singer and Dr. Robert Roy, Dean and Vice-Dean Academic respectively, of Arts and Science allocated funds to construct an instrument room for biotechnology, a bioinformatics laboratory, a room for a computational server, and a microscopy room (to house a laser scanning confocal microscope, a fluorescence microscope and a micromanipulator). Construction began in late January under the supervision of Mr. Marc-Andre Loignon, an architect of Facilities and Planning. Mr. Claude Lamarche, the technical officer of Arts and Science, assisted in the acquisition of ...,, furniture. Major structural changes were completed in early April. Minor alterations continue as instruments are being installed. As we had excellent and close working relationships with Mr. Loignon and Mr. Lamarche, construction of the laboratories proceeded very smoothly and to specifications. i The current arrangment is a temporary home for the facility. We are expected to move into the new science complex at Loyola campus in 2002-2003. The Centre has been allocated over 7,000 square feet of laboratory and office space. It will have the following components: a biotechnology laboratory with two coldrooms and a radioisotope facility; three instrument rooms; a bioinformatics laboratory; a room for computational servers; an image facility with a darkroom and two microscope rooms; two environmental rooms for plant tissue culture and transfer; a level 3 containment facility; a cell technology facility with a kitchen, cell culture rooms and a preparation area; and an office suite. Additional details of the planned facility can be found in Appendix I. 6 Research Support Infrastructure grant: With the donations from BioChem Pharma, Inc. and Dr. F. Bellini as matching funds we applied for an institutional innovation grant from the Canada Foundation for Innovation (CFI). We were awarded $1,246,080 by CFI and a matching $1,246,080 by the Ministry of Education of Quebec. Seven hundred thousand dollars of the award are to be spent on the construction of the new facility, and the remaining for equipment acquisition. Research grants and contracts: Research support for members (underlined) of the Centre are listed below in alphabetical order. Gulick, P., NSERC Research Grant "Siganlling and the genetics of salt stress tolernace in Lophopyrum elongatum and breat wheat", 2000-2004, $32,000/year Ibrahim, R., NSERC Research Grant, "Biochemistry and molecular biology of plant metabolism", 1998-2002, $51, 750/year. il Ibrahim, R., Natural Resources Canada, "Purification and characterization of a novel flavonol dioxygenase", 1999-2000, $12,000/year Ibrahim, R., Natural Resources Canada, "Molecular cloning and functional expression of a flavonol glucosidase acyltransferase", 2000-2001, $15,000 Joyce, P., NSERC Research Granl, 'Prolein largeling in planl cells', 1999-2003, $38,745/year Joyce, P. and Pawlowski, .. J., NSERC Genomics Grant, "Stnir.tr 1ml Anrl functional ~enomics of aromatic degradation in the model yeast, Trichosporon cutaneum", 2000-2003, $76 500/year Matton, D., Gulick, P. and Brisson, N. NSERC Genomics Grant, "Genomic analysis of signaling during embryogenesis and defense response in potato", 2000-2003, $·I 54,000/year Pawlowski, J., NSERC Operating Grant, "Molecular mechanisms of bacterial phenol degradation and mercuric ion detoxification", 1998-2002, $42,000/year Eltis, L., Sylvestre, M., Pawlowski, J. and Snieckus, V., NSERC Strategic Grant, "Engineering metabolic pathways for PCB degradation", 1999-2002, $27 4,070/year Peslherbe, G., Gadosy, T., Pawlowski, J. and Turnbull, J., GHJ· (Concordia), 7 "Graphics workstation for molecular modeling", 1999-2000, $7000/year Sarhan, F., Gulick, P., Huener, N., Fowler, B. and Simmonds, J. NSERC Genomics Grant, " Functional genomics and mapping of stress regulated genes in cereals", 2000-2003, $114,000/year Storms, R., NSERC Research Grant, "Gene expression in Saccharomyces cerevisiae", 1999-2003, $31,680/year Storms, R., Mycota Biosciences research contract, $30,000 Storms, R., Bussey, H. (P.I.), MRC Operating Grant, "A complete set of yeast gene disruptions", $154,000/year, 1998-2001 Storms, R. and Tsang, A. NSERC Collaborative Research & Development Grant, "Expression systems for Aspergillus niger", 1998-2001, $108,000/year Storms, R., Bussey, H. and Tsang, A., FCAR Team Grant, "Genome wide approaches to determining gene function in model eukaryotes, 1998-2001, $45,000/year Tsang, A. NSERC Research Grant, "Protein-protein interaction", 1997-2001, 23,000/year Tsang, A. Gist-brocades (DSM Biologics) research contract US$50,000 Tsang, A., Butler, G, Joyce, P., Lam, C., Storms, R. and Turnbull, J., FRDP Inter-disciplinary Grant, "Bioinformatics infrastructure for genomics research", 1997-99, 45,000/year Jymbull, J.L., NSERC Rese8rr:h Grnnt, "ActivP. SitP. St11rliP.s nn M11lti-nnmain Enzymes", 1997-2001, $37,653/year Varin, L., NSERC Research Grant, "Biochemistry and molecular biology of enzymatic sulfation in plants", 1998-2002, 52, 100/year Varin, L., Novartis research contract, 144,000/year 8 Equipment Acquisition One of the main responsibilities of the Centre is to manage the BioChem Pharma Genomics Facility. Acquisition of large and small equipment constitutes the major activity in our first year of operation. Purchase of large instruments involved all members of the Centre and was a multi-step process. First we identified all available manufacturers and compared the specifications of the instruments. We attended workshops and demonstrations of the instruments. Where feasible we gained hands-on experience with the instruments. This process can be illustrated by the acquisition of the laser scanning confocal microscope. We formed an ad hoc committee made up of Ors. P. Joyce, R. Storms and A. Tsang. We also asked two outside experts of confocal microscopy, Dr. Paul Lasko and Dr. Beat Suter of the Biology Department of McGill University, to assist us in making our evaluation. We examined the specifications of available confocal microscopes and identified two models. We invited technical experts of the two manufacturers to present formal workshops. The workshops were attended by members of the Centre as well as researchers from Biology (Concordia and McGill), Chemistry and Biochemistry, and Psychology. For one manufacturer, a hands-on demonstration was held at Concordia for one week. Ors. Lasko and Suter had in-depth knowledge of the other model. We decided on the specifications and then sought the help of the Purchasing Department to seek tenders and the best price. The purchase of each major instrument was an elaborate process that took as long as 6 months. It also involved the training of support staff. Listed below are major pieces of equipment acquired in the past year. !EQUIPMENT I LOCATION Leica laser scanning confocal microscope 1223-2 Beckman Optima XLI analytical ulracentrifuQe 1221 Beckman J-201 high capacity centrifuge 1??1 Beckman J-301 superspeed centrifuge 1221 Capillary electr.QPhoresis autom~!_~d DNA sequencer 1221 ESI ON/\ Micro arrayor 1221 ls9thermal titration microcalorimeter (Microcal) 1221 Fluorescence & visible imaQinQ system 1239 Multitask plate reader (fluorescence/ luminescence/ 1221 absorption) Micromanipulator (Singer) 1223-1 Pulse-field electrophoresis chiller system (BioRad) ·122·1 Envi1011me11lc::1I sllc::1ke1s (2X) 1221 Computer workstations (10 stations and servers) 1221/ 1223/ 1239 ---·- ...... --......... -·. ,. ~· - - ••:•·· < 9